Soulsilver- And note in the Crystal Onix Tracy yells at the poor thing and blames it and then we don't see Venonat for quite some time after it, I think Tracy stopped trusting it and used Marill more because of it.
Nemmeh- That chef in Go West Young Meowth makes me furious, if I saw someone chasing a cat down the street or any animal threatening to slam it with a pan just because it was starving I would grab that pan and slam his head with it, see how he likes it (I hope Persian and the other Meowths kept making life difficult for him).
Misty's Goldeen, Brock's Zubat and Vulpix are just a few. Psyduck got quite annoying after everytime Misty would send a Pokemon out it would appear instead, it's barely Misty's fault half of the time.
WT- About that, people have got to realize AJ, Samurai etc are all in a different region, or probably went somewhere else. So it's not like it would be easy for him to find them, is he going to leave in the middle of Johto/Hoenn etc to find them? No because he does have a journey of his own, they have to actually go back to the place they found them. Sure they probably didn't go where AJ or Primeape in Kanto (Haunter in Saffron though.. The Battle Frontier whoever it was again Lucy I think was right in Saffron so he could have seen Haunter again). And Pidgeot, Viridian Forest don't get me started